Structure Unifies the Viral Universe

Objectives…  describe the current status of structural work  highlighting its power to infer common ancestry  discuss the limitations and obstacles ahead of us  provide high-throughput methods to facilitate the large-scale sampling of the virosphere.

Is it possible to meaningfully comprehend the diversity of the viral world? although there is immense genomic variation, every infective virion is restricted by strict constraints in structure space.  number of ways to fold a protein chain  small subset of these have the potential to construct a virion

General characteristics &structure of viruses  Viruses are smaller than bacteria, they range in size between nanometer  Viruses contain only one type of nucleic acid, either DNA or RNA, but never both.  Viruses consist of nucleic acid acid surrounded by a protein coat called capsid.  The capsid is composed of small structural units called capsomeres.  The capsid protects nucleic acid from inactivation by the outer physical conditions.  Some viruses have additional lipoprotein envelope, composed of virally coded protein and host lipid.  The viral envelope is covered with glycoprotein spikes.  Some viruses have enzymes inside the virion. Viruses do NOT multiply in chemically defined media.  Viruses do NOT undergo binary fission.  Viruses lack cellular organelles, such as mitochondria and ribosomes.  Viruses are obligate cellular parasite( they replicate only inside living cells)  Viruses replicate through replication of their nucleic acid and synthesis of the viral protein.  All ss- RNA viruses with negative polarity have the enzyme transcriptase

copyright cmassengale5 Viral Structure

Viral Shapes  Viruses come in a variety of shapes  Some may be helical shape like the Ebola virus  Some may be polyhedral shapes like the influenza virus  Others have more complex shapes like bacteriophages

7copyright cmassengale HELICAL VIRUSES  The virus particle is elongated or pleomorphic (not spherical), and the nucleic acid is spiral. Caposomeres are arranged round the nucleic acid.  The following virus families have helical symmetry :  Orthomyxoviridae,paramyxoviridae,rhabdoviri dae, filoviridae

 12 vertices  20 faces  (equilateral triangles)  symmetry axes  60 identical* subunits  in identical environments  can form icosahedral shell  Adenoviridae, Reoviridae 8copyright cmassengale POLYHEDRAL VIRUSES

Icosahedral Symmetry

COMPLEX VIRUSES  Bacteriophage.  Capsid(head) is polyhedral, tail sheath is helical.  Tail fibers, plate and pin.  Large (300 nm), complicated structure

origins of viruses  (a ) Viruses originated from times before cellular life was invented  (b) viruses originated from cells by reduction  (c) viruses escaped from cells by utilizing cellular replicative elements removed from cellular control.

VIRUS CLASSIFICATION  Baltimore classification: The Baltimore classification of viruses is based on the mechanism of mRNA production. I: dsDNA viruses (e.g. Adenoviruses, Herpesviruses, Poxviruses) II: ssDNA viruses (+ strand or "sense") DNA (e.g. Parvoviruses) III: dsRNA viruses (e.g. Reoviruses) IV: (+)ssRNA viruses (+ strand or sense) RNA (e.g. Picornaviruses, Togaviruses) V: (−)ssRNA viruses (− strand or antisense) RNA (e.g. Orthomyxoviruses, Rhabdoviruses) VI: ssRNA-RT viruses (+ strand or sense) RNA with DNA intermediate in life-cycle (e.g. Retroviruses) VII: dsDNA-RT viruses (e.g. Hepadnaviruses)

Steps in virus replications : - Adsorption (attachment). - Penetration. - uncoating. - Replication of the viral genome. - Transcription of the viral genome into m-RNA. - Translation of m-RNA into viral proteins. - protein synthesis, - Viral assembly.

ICTV classification  The International Committee on Taxonomy of Viruses (ICTV) developed the current classification system  The general taxonomic structure is as follows:  Order (-virales)  Family (-viridae)  Subfamily (-virinae)  Genus (-virus)  Species (-virus)

LESSONS FROM EARLY STRUCTURES  Tobacco mosaic virus (TMV)  Tobacco necrosis virus  Tomato bushy stunt virus  Poliovirus  Insect virus  adenovirus  bacterial virus (PRD1) These observations inspired us to develop a systematic approach to identifying lineages of viruses on the basis of virion architecture, with the expectation that these lineages may have separate but ancient origins.

PROBLEMS OF COINCIDENCE AND ANALOGY  argument above suggests that structure based lineages may tend to reflect homology rather than structural convergence  Occurrences of folds, such as the β-barrel, might reflect analogy (convergence) rather than homology(divergence)

TOOLS FOR STRUCTURE-BASED PHYLOGENY Marked sequence similarity between the target proteins, allowing them to be aligned, can be translated into an evolutionary distance, and when a full pair wise comparison is performed between a series of sequences, the results can be represented as a phylogenetic tree.  MODELLER  SWISS-MODEL SWISS-MODEL

VIRION ARCHITECTURE COUPLES TO GENOME PACKAGING

P22 Pathway

CURRENT STATUS: DETECTING VIRAL LINEAGES

Structure-based phylogenetic tree for the dsRNA lineage of viruses

Structure-based phylogenetic tree of nucleocapsid proteins Suggesting that the nucleoprotein may be useful as a marker for the vertically inherited component defining the viral self within these groups of viruses

Tanks for attention

Evolution of dsDNA viruses  All known viruses, whether infecting bacteria or humans, may have evolved from a single common ancestor, relatively early in the evolution of organisms.

Overview of a packasome assembly in DNA or RNA phages. (A) Overview of a ‘generic’ packasome formed by class 1 (dsDNA) phages. Linear genomic DNA undergoes an ATP-dependent translocation by a multimeric (5–6 copies) large terminase subunit protein engaged with the dodecameric portal of the prohead. The small terminase subunit (8–11 copies) is required for initiating packaging on the concatemer, but is frequently non-essential and even inhibitory to active DNA translocation. (B) RNA packaging in class 3 (dsRNA) phages. The genome of Cystoviridae such as the Pseudomonas phages f6–f13 comprises three RNA segments, named Small, Medium and Large (S, M and L). The three RNA segments are generated in ss form during phage maturation. A hexameric P4 phage protein permanently occupies procapsid vertices, whereas the major procapsid structural protein selects 50 pac site ssRNAs for packaging. Packaging is catalyzed by the NTP-driven P4 hexameric motor and synthesis of the second RNA strand of each genome segment occurs within the head subsequent to RNA packaging

Common steps in the assembly of all dsDNA viruses  Unique portal ring at one Vertex  Scaffolding proteins  Procapsid assembled empty of DNA  DNA pumped into procapsid through portal ring  DNA moves back through portal to enter cell